Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000190.1 Hibiscus syriacus cultivar Beakdansim tig00000340_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 14308945
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 62
Found at i:2980606 original size:7 final size:7
Alignment explanation
Indices: 2980589--2980625 Score: 65
Period size: 7 Copynumber: 5.1 Consensus size: 7
2980579 AACTCAAAAT
2980589 AATATTTA
1 AATA-TTA
2980597 AATATTA
1 AATATTA
2980604 AATATTA
1 AATATTA
2980611 AATATTA
1 AATATTA
2980618 AATATTA
1 AATATTA
2980625 A
1 A
2980626 TCTAATTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 25 0.86
8 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
AATATTA
Found at i:2980648 original size:16 final size:16
Alignment explanation
Indices: 2980600--2980645 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 16
2980590 ATATTTAAAT
*
2980600 ATTAAATATTAA-AT-
1 ATTAAATATTAATCTA
2980614 ATTAAATATTAATCTA
1 ATTAAATATTAATCTA
*
2980630 ATTAAA-ATTATTCTA
1 ATTAAATATTAATCTA
2980645 A
1 A
2980646 ATTTTAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 12 0.43
15 10 0.36
16 6 0.21
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (16 bp):
ATTAAATATTAATCTA
Found at i:2981806 original size:16 final size:17
Alignment explanation
Indices: 2981785--2981818 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2981775 AATATATTAT
2981785 AAAAAT-TTAAAATTTA
1 AAAAATATTAAAATTTA
*
2981801 AAAAATATTAAATTTTA
1 AAAAATATTAAAATTTA
2981818 A
1 A
2981819 TTTTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAAAATATTAAAATTTA
Found at i:2982465 original size:256 final size:258
Alignment explanation
Indices: 2981965--2982462 Score: 778
Period size: 256 Copynumber: 1.9 Consensus size: 258
2981955 CTCCATCCGA
2981965 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCTGAATATATGAATTAGAAACCCGAC
1 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGA-CT--ATATATGAATTAGAAA--C-AC
2982030 CCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAAAAGTGACTTAATTGAAAAAATAT
60 CCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAAAAGTGACTTAATTGAAAAAATAT
* *
2982095 ATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATCTATTTTTTGGG
125 ATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTTTTCGGG
* * *
2982160 TCGGGTCGAGTCGGGTATTTTTTACCCTAAACCCGAACCCGACCCGACCCTAATATCACACTTAA
190 TCGGGT---GTCAGGTATTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCACACTTAA
2982225 AAAAACC
252 AAAAACC
*
2982232 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGA-T-TATATGAATTAG-AA-ATCCGACC
1 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACTATATATGAATTAGAAACACCCGACC
*
2982293 CGAAATAAT-AAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAT-TATATAT
66 CGAAATAATAAAAAAATTATTTTTATTCAATAAAAAAAGTGACTTAATTGAAAAAATATATATAT
2982356 AGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTCGGGTCGGG
131 AGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATAT-TTTTCGGGTCGGG
*
2982421 T-T-AGGTATTTTTCACCCTAAACCCGAACTCGACCCGACCCGA
195 TGTCAGGTATTTTTCACCCTAAACCCGAACCCGACCCGACCCGA
2982463 CCCGAATATA
Statistics
Matches: 222, Mismatches: 8, Indels: 18
0.90 0.03 0.07
Matches are distributed among these distances:
251 36 0.16
252 1 0.00
255 57 0.26
256 59 0.27
257 16 0.07
261 2 0.01
262 12 0.05
265 1 0.00
267 38 0.17
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.28
Consensus pattern (258 bp):
GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACTATATATGAATTAGAAACACCCGACC
CGAAATAATAAAAAAATTATTTTTATTCAATAAAAAAAGTGACTTAATTGAAAAAATATATATAT
AGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTTTTCGGGTCGGGT
GTCAGGTATTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCACACTTAAAAAAACC
Found at i:2986963 original size:2 final size:2
Alignment explanation
Indices: 2986958--2987022 Score: 102
Period size: 2 Copynumber: 34.5 Consensus size: 2
2986948 AGAAATAAAA
2986958 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2986999 AT AT AT A- AT AT A- AT A- AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2987023 ATAAAAATAA
Statistics
Matches: 59, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
1 4 0.07
2 55 0.93
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2989148 original size:112 final size:112
Alignment explanation
Indices: 2988998--2989422 Score: 715
Period size: 112 Copynumber: 3.8 Consensus size: 112
2988988 AACTGGGAAA
* * *
2988998 TTGTTTGTTGACAGCCAGTCGCCCCTTCGCTGTAAAGTTGAGCTTGTACTGTCTCGAGTCTAATA
1 TTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGTCTAATA
2989063 TCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAAAG
66 TCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAAAG
* *
2989110 TTGTTTGTTGACAGTCAGTCGCCCCTTAGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCTAATA
1 TTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGTCTAATA
* *
2989175 TCATTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAAAG
66 TCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAAAG
2989222 TTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGTCTAATA
1 TTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGTCTAATA
* *
2989287 TCCTTCGCTGTGAAGTTGAAATTGACTCTAAATGAAACTGACAAAAG
66 TCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAAAG
* * * * * *
2989334 TTATTTATTGACAGTCAGCCGCCCTTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATA
1 TTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGTCTAATA
2989399 TCCTTCGCTGTGAAGTTGAAATTG
66 TCCTTCGCTGTGAAGTTGAAATTG
2989423 GATCTAAAAC
Statistics
Matches: 294, Mismatches: 19, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
112 294 1.00
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (112 bp):
TTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGTCTAATA
TCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAAAG
Found at i:2990478 original size:18 final size:18
Alignment explanation
Indices: 2990455--2990489 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2990445 CCCTTTCAGG
*
2990455 TTTTCAACTTGGACCCAT
1 TTTTCAACTTGAACCCAT
*
2990473 TTTTCATCTTGAACCCA
1 TTTTCAACTTGAACCCA
2990490 CCTTATTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.29, G:0.09, T:0.40
Consensus pattern (18 bp):
TTTTCAACTTGAACCCAT
Found at i:2990513 original size:7 final size:7
Alignment explanation
Indices: 2990501--2990534 Score: 50
Period size: 8 Copynumber: 4.6 Consensus size: 7
2990491 CTTATTTTTC
2990501 TTTTCTT
1 TTTTCTT
2990508 TTTTCTT
1 TTTTCTT
2990515 TTGTTCTT
1 TT-TTCTT
2990523 TTGTTCTT
1 TT-TTCTT
2990531 TTTT
1 TTTT
2990535 TTAAATTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 11 0.42
8 15 0.58
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (7 bp):
TTTTCTT
Found at i:2990523 original size:8 final size:8
Alignment explanation
Indices: 2990503--2990532 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
2990493 TATTTTTCTT
2990503 TTCTTTT-
1 TTCTTTTG
2990510 TTCTTTTG
1 TTCTTTTG
2990518 TTCTTTTG
1 TTCTTTTG
2990526 TTCTTTT
1 TTCTTTT
2990533 TTTTAAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (8 bp):
TTCTTTTG
Found at i:2990531 original size:16 final size:15
Alignment explanation
Indices: 2990501--2990534 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2990491 CTTATTTTTC
2990501 TTTTCTTTT-TTCTT
1 TTTTCTTTTGTTCTT
2990515 TTGTTCTTTTGTTCTT
1 TT-TTCTTTTGTTCTT
2990531 TTTT
1 TTTT
2990535 TTAAATTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 2 0.11
15 9 0.50
16 7 0.39
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (15 bp):
TTTTCTTTTGTTCTT
Found at i:3001194 original size:23 final size:23
Alignment explanation
Indices: 3001168--3001249 Score: 137
Period size: 23 Copynumber: 3.6 Consensus size: 23
3001158 CTCGTATAAA
*
3001168 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCGCGTAGAAT
* *
3001191 TGCACCGAAGTGCCGTGTAAAAT
1 TGCACCGAAGTGCCGCGTAGAAT
3001214 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCGCGTAGAAT
3001237 TGCACCGAAGTGC
1 TGCACCGAAGTGC
3001250 TATATAAAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCGCGTAGAAT
Found at i:3001258 original size:46 final size:46
Alignment explanation
Indices: 3001168--3001259 Score: 148
Period size: 46 Copynumber: 2.0 Consensus size: 46
3001158 CTCGTATAAA
* *
3001168 TGCACCGAAGTGCCACGTAGAATTGCACCGAAGTGCCGTGTAAAAT
1 TGCACCGAAGTGCCACGTAGAATTGCACCGAAGTGCCATATAAAAT
* *
3001214 TGCACCGAAGTGCCGCGTAGAATTGCACCGAAGTGCTATATAAAAT
1 TGCACCGAAGTGCCACGTAGAATTGCACCGAAGTGCCATATAAAAT
3001260 GTCCCTAAGG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.21
Consensus pattern (46 bp):
TGCACCGAAGTGCCACGTAGAATTGCACCGAAGTGCCATATAAAAT
Found at i:3004108 original size:20 final size:20
Alignment explanation
Indices: 3004083--3004130 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
3004073 ATTTCATTTC
3004083 TTTATTCCATTCTTCCTTTA
1 TTTATTCCATTCTTCCTTTA
3004103 TTTATTCCATTCTTCCTTTA
1 TTTATTCCATTCTTCCTTTA
3004123 TTTATTCC
1 TTTATTCC
3004131 TTATACACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.15, C:0.25, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTATTCCATTCTTCCTTTA
Found at i:3006243 original size:23 final size:23
Alignment explanation
Indices: 3006217--3006275 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
3006207 CTCGTATAAA
3006217 TGCACCAAAGTGCCACGTAGAAT
1 TGCACCAAAGTGCCACGTAGAAT
*
3006240 TGCACCAAAGTGCCGCGTAGAAT
1 TGCACCAAAGTGCCACGTAGAAT
*
3006263 TGCACCGAAGTGC
1 TGCACCAAAGTGC
3006276 TATATAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.17
Consensus pattern (23 bp):
TGCACCAAAGTGCCACGTAGAAT
Found at i:3007900 original size:21 final size:21
Alignment explanation
Indices: 3007876--3007920 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3007866 TCTAGTTCGT
* * *
3007876 TTGAGGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
3007897 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
3007918 TTG
1 TTG
3007921 CCCAGAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.13, C:0.24, G:0.31, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:3015418 original size:20 final size:20
Alignment explanation
Indices: 3015370--3015419 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
3015360 TTAAGAACAA
*
3015370 TATCAATATTATTTTATTAG
1 TATCAATATTATTTTATCAG
* **
3015390 CATTGATATTATTTTATCAG
1 TATCAATATTATTTTATCAG
3015410 TATCAATATT
1 TATCAATATT
3015420 TTATCTTCGA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.34, C:0.08, G:0.06, T:0.52
Consensus pattern (20 bp):
TATCAATATTATTTTATCAG
Found at i:3015549 original size:10 final size:10
Alignment explanation
Indices: 3015504--3015550 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
3015494 TATGGCAAAA
3015504 ATTTAAA-TT
1 ATTTAAATTT
3015513 ATTTAATATTT
1 ATTTAA-ATTT
*
3015524 ATATAAATTT
1 ATTTAAATTT
3015534 -TATTAAATTT
1 AT-TTAAATTT
3015544 ATTTAAA
1 ATTTAAA
3015551 ATAAATTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
9 7 0.22
10 17 0.53
11 8 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
ATTTAAATTT
Found at i:3017736 original size:21 final size:21
Alignment explanation
Indices: 3017692--3017735 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3017682 AAATTACACA
* *
3017692 TTTAGTATCTAAACTATTAAT
1 TTTAGTACCTAAACTATCAAT
3017713 TTTAGTACCTAAACT-TCAAT
1 TTTAGTACCTAAACTATCAAT
3017733 TTT
1 TTT
3017736 TTTTTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.34, C:0.14, G:0.05, T:0.48
Consensus pattern (21 bp):
TTTAGTACCTAAACTATCAAT
Found at i:3022824 original size:23 final size:23
Alignment explanation
Indices: 3022798--3022842 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3022788 CACCACAGCT
* *
3022798 CGTATAATTGCATCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
3022821 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
3022843 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:3023063 original size:149 final size:149
Alignment explanation
Indices: 3022818--3023124 Score: 553
Period size: 149 Copynumber: 2.1 Consensus size: 149
3022808 CATCGAAGTG
3022818 CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAG
1 CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAG
** *
3022883 AATCATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCACAGAAT
66 AATCATATACATATGCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTTCCAAAGAAT
3022948 ATATATATATCCCGAAGGA
131 ATATATATATCCCGAAGGA
*
3022967 CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAG
1 CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAG
*
3023032 AATCATATACATATGCTAGGGATCATA-TATGTGTCTCACCAGACTTCACACATGTTCCAAAGAA
66 AATCATATACATATGCTAGGGATCA-AGTATGTGTCTCACAAGACTTCACACATGTTCCAAAGAA
3023096 TATATATATATCCCGAAGGA
130 TATATATATATCCCGAAGGA
3023116 CCGCGTAGA
1 CCGCGTAGA
3023125 CCCTCGACTC
Statistics
Matches: 152, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
149 151 0.99
150 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAG
AATCATATACATATGCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTTCCAAAGAAT
ATATATATATCCCGAAGGA
Found at i:3024043 original size:18 final size:18
Alignment explanation
Indices: 3024022--3024056 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3024012 TCCCATCTAG
3024022 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
3024040 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
3024057 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:3024648 original size:65 final size:66
Alignment explanation
Indices: 3024548--3024673 Score: 211
Period size: 65 Copynumber: 1.9 Consensus size: 66
3024538 TAATGAAGGT
3024548 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAATGGG
1 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAATGGG
3024613 G
66 G
* *
3024614 ATGCATCGATGCACT-C-CTTATGCATTGATGCATAAATCCTATTCGATGTTTTCTATTTAA
1 ATGCATCGATGCACTACAC-CATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAA
3024674 ATTCATGCAT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
64 1 0.02
65 41 0.72
66 15 0.26
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.37
Consensus pattern (66 bp):
ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAATGGG
G
Found at i:3027434 original size:15 final size:15
Alignment explanation
Indices: 3027414--3027442 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3027404 AGAAAATTTG
3027414 AAAATTAAAGAAAAC
1 AAAATTAAAGAAAAC
3027429 AAAATTAAAGAAAA
1 AAAATTAAAGAAAA
3027443 GAAGAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.76, C:0.03, G:0.07, T:0.14
Consensus pattern (15 bp):
AAAATTAAAGAAAAC
Found at i:3042489 original size:17 final size:16
Alignment explanation
Indices: 3042445--3042497 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
3042435 ATTCATGTCC
**
3042445 ATTTTAAAATTTAAAT
1 ATTTTAAAATTTATTT
*
3042461 ATTTTATTAATTGTATTT
1 ATTTTA-AAATT-TATTT
3042479 ATTTTAAAATTTTATTT
1 ATTTTAAAA-TTTATTT
3042496 AT
1 AT
3042498 ACATGTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
16 6 0.20
17 13 0.43
18 11 0.37
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
ATTTTAAAATTTATTT
Found at i:3043190 original size:19 final size:20
Alignment explanation
Indices: 3043166--3043205 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
3043156 TAAGGTAAAA
3043166 TTATTTTA-ATTAT-ATTATT
1 TTATTTTATA-TATGATTATT
3043185 TTATTTTATATATGATTATT
1 TTATTTTATATATGATTATT
3043205 T
1 T
3043206 GAAAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (20 bp):
TTATTTTATATATGATTATT
Found at i:3046424 original size:11 final size:11
Alignment explanation
Indices: 3046408--3046434 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
3046398 TCTTTATGTT
3046408 ATTTAATTTTC
1 ATTTAATTTTC
3046419 ATTTAATTTTC
1 ATTTAATTTTC
3046430 ATTTA
1 ATTTA
3046435 CTTTCAGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (11 bp):
ATTTAATTTTC
Found at i:3046765 original size:3 final size:3
Alignment explanation
Indices: 3046751--3046803 Score: 70
Period size: 3 Copynumber: 17.7 Consensus size: 3
3046741 TCACTATCTC
* * * *
3046751 CAT CAT CGT CAT CAT CAT CAT CAT CAT CAA CAT CAT CAT CTT CAC CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
3046799 CAT CA
1 CAT CA
3046804 GGAGCAGATA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.32, C:0.36, G:0.02, T:0.30
Consensus pattern (3 bp):
CAT
Found at i:3048705 original size:34 final size:33
Alignment explanation
Indices: 3048667--3048732 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 33
3048657 CCTAATTTAA
*
3048667 TAAAT-ATTATAGAAATTAAAATATAAACTAATAC
1 TAAATAATTAAAGAAA-TAAAATATAAAC-AATAC
* *
3048701 TAAATAATTAAATAAATAAAATATTAACAATA
1 TAAATAATTAAAGAAATAAAATATAAACAATA
3048733 ATTAAAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 4 0.14
34 16 0.57
35 8 0.29
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.32
Consensus pattern (33 bp):
TAAATAATTAAAGAAATAAAATATAAACAATAC
Found at i:3049025 original size:22 final size:22
Alignment explanation
Indices: 3049000--3049045 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
3048990 TTTGAATGAA
3049000 GAGGGGATGGGGGTATTTATAG
1 GAGGGGATGGGGGTATTTATAG
3049022 GAGGGGATGGGGGTATTTATAG
1 GAGGGGATGGGGGTATTTATAG
3049044 GA
1 GA
3049046 AGAGATGAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.24, C:0.00, G:0.50, T:0.26
Consensus pattern (22 bp):
GAGGGGATGGGGGTATTTATAG
Found at i:3049052 original size:22 final size:22
Alignment explanation
Indices: 3049005--3049058 Score: 81
Period size: 22 Copynumber: 2.4 Consensus size: 22
3048995 ATGAAGAGGG
* *
3049005 GATGGGGGTATTTATAGGAGGG
1 GATGGGGGTATTTATAGGAAGA
3049027 GATGGGGGTATTTATAGGAAGA
1 GATGGGGGTATTTATAGGAAGA
3049049 GATGAGGGGT
1 GATG-GGGGT
3049059 TAGTCGAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 24 0.83
23 5 0.17
ACGTcount: A:0.26, C:0.00, G:0.48, T:0.26
Consensus pattern (22 bp):
GATGGGGGTATTTATAGGAAGA
Found at i:3049841 original size:15 final size:17
Alignment explanation
Indices: 3049823--3049861 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
3049813 TCAAAATTAA
3049823 AAAAATTATT-ATTT-T
1 AAAAATTATTAATTTAT
*
3049838 AAAAAATATTAATTTAT
1 AAAAATTATTAATTTAT
3049855 AAAAATT
1 AAAAATT
3049862 GTATGGTAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 9 0.45
16 4 0.20
17 7 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAAAATTATTAATTTAT
Found at i:3049843 original size:16 final size:16
Alignment explanation
Indices: 3049817--3049861 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
3049807 TTCAAATCAA
*
3049817 AATTAAAAAAATTATT
1 AATTTAAAAAATTATT
*
3049833 ATTTTAAAAAA-TATT
1 AATTTAAAAAATTATT
3049848 AATTTATAAAAATT
1 AATTTA-AAAAATT
3049862 GTATGGTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 9 0.38
16 14 0.58
17 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AATTTAAAAAATTATT
Found at i:3054909 original size:2 final size:2
Alignment explanation
Indices: 3054902--3054940 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3054892 GTTATCGTTC
*
3054902 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3054941 GAGAGAGAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3054967 original size:4 final size:4
Alignment explanation
Indices: 3054960--3054993 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
3054950 ATATGTGTGC
3054960 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
3054994 CCCAACATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:3055075 original size:44 final size:42
Alignment explanation
Indices: 3054976--3055101 Score: 152
Period size: 44 Copynumber: 3.0 Consensus size: 42
3054966 GTATGTATGT
* * *
3054976 ATGTATGTATGTATGTATCCCAACATATATATAT-TATAGATGA
1 ATGTATG-ATG-ATGTATCCCAATATATATAGATAGATAGATGA
3055019 ATGTATG-T-ATGTATCCCAATATATATAGATAGATAGAT-A
1 ATGTATGATGATGTATCCCAATATATATAGATAGATAGATGA
3055058 GATGTATGCATGCATGTATCCCAATATATATAGATAGATAGATG
1 -ATGTATG-ATG-ATGTATCCCAATATATATAGATAGATAGATG
3055102 TATGCATGTA
Statistics
Matches: 73, Mismatches: 3, Indels: 12
0.83 0.03 0.14
Matches are distributed among these distances:
39 21 0.29
40 13 0.18
41 1 0.01
42 1 0.01
43 7 0.10
44 30 0.41
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (42 bp):
ATGTATGATGATGTATCCCAATATATATAGATAGATAGATGA
Found at i:3063988 original size:38 final size:38
Alignment explanation
Indices: 3063937--3064013 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
3063927 GATATTCGGA
3063937 ATAGTTCATAAAGAATTCAAGCATCCAAAGAGGACAAT
1 ATAGTTCATAAAGAATTCAAGCATCCAAAGAGGACAAT
3063975 ATAGTTCATAAAGAATTCAAGCATCCAAAGAGGACAAT
1 ATAGTTCATAAAGAATTCAAGCATCCAAAGAGGACAAT
3064013 A
1 A
3064014 ACTGATGGCG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.21
Consensus pattern (38 bp):
ATAGTTCATAAAGAATTCAAGCATCCAAAGAGGACAAT
Found at i:3076581 original size:16 final size:17
Alignment explanation
Indices: 3076560--3076594 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
3076550 TTACTATTCA
3076560 CGTGAATAGTG-AATTT
1 CGTGAATAGTGAAATTT
3076576 CGTGAATAGTGAAATTT
1 CGTGAATAGTGAAATTT
3076593 CG
1 CG
3076595 GTCGGCGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (17 bp):
CGTGAATAGTGAAATTT
Found at i:3077352 original size:15 final size:16
Alignment explanation
Indices: 3077332--3077364 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3077322 GTGGCAGATC
3077332 AAAATCCAG-ACGGGA
1 AAAATCCAGAACGGGA
*
3077347 AAAATCTAGAACGGGA
1 AAAATCCAGAACGGGA
3077363 AA
1 AA
3077365 GAAAGATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.15, G:0.24, T:0.09
Consensus pattern (16 bp):
AAAATCCAGAACGGGA
Found at i:3081923 original size:15 final size:15
Alignment explanation
Indices: 3081903--3081936 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
3081893 CCACAAACGG
3081903 TTATTAGTGTTTTTC
1 TTATTAGTGTTTTTC
3081918 TTATTAGTGTTTTTC
1 TTATTAGTGTTTTTC
3081933 TTAT
1 TTAT
3081937 AAATGTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.15, C:0.06, G:0.12, T:0.68
Consensus pattern (15 bp):
TTATTAGTGTTTTTC
Found at i:3081943 original size:15 final size:15
Alignment explanation
Indices: 3081910--3081943 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3081900 CGGTTATTAG
* *
3081910 TGTTTTTCTTATTAG
1 TGTTTTTCTTATAAA
3081925 TGTTTTTCTTATAAA
1 TGTTTTTCTTATAAA
3081940 TGTT
1 TGTT
3081944 ATAAGGAAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.06, G:0.12, T:0.65
Consensus pattern (15 bp):
TGTTTTTCTTATAAA
Found at i:3082411 original size:17 final size:16
Alignment explanation
Indices: 3082389--3082442 Score: 56
Period size: 17 Copynumber: 3.3 Consensus size: 16
3082379 CCGTGTCCCG
*
3082389 ACCCGGATGTTACGGGT
1 ACCCGGATATT-CGGGT
*
3082406 ACCCGG-TAATCGGGT
1 ACCCGGATATTCGGGT
*
3082421 ACCCGGATTTTGCGGGT
1 ACCCGGATATT-CGGGT
3082438 ACCCG
1 ACCCG
3082443 ATACCCGGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 11 0.35
16 4 0.13
17 16 0.52
ACGTcount: A:0.17, C:0.28, G:0.33, T:0.22
Consensus pattern (16 bp):
ACCCGGATATTCGGGT
Found at i:3087511 original size:3 final size:3
Alignment explanation
Indices: 3087503--3087590 Score: 169
Period size: 3 Copynumber: 29.7 Consensus size: 3
3087493 CAAACAAACG
3087503 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
3087551 TTC TTC TTC TTC TTC TTC -TC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
3087591 GTCTTGCTAT
Statistics
Matches: 84, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.02
3 82 0.98
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:3089486 original size:20 final size:21
Alignment explanation
Indices: 3089454--3089492 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
3089444 ATAACATAAA
*
3089454 ATAAAATAAAATTTAAATATT
1 ATAAAATAAAATTAAAATATT
3089475 ATAAAA-AAAATTAAAATA
1 ATAAAATAAAATTAAAATA
3089493 AATAAACCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAAAATAAAATTAAAATATT
Found at i:3089497 original size:19 final size:20
Alignment explanation
Indices: 3089452--3089498 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
3089442 CAATAACATA
*
3089452 AAATAAAATAAAATTTAAAT
1 AAATAAAATAAAATTAAAAT
*
3089472 ATTATAAAA-AAAATTAAAAT
1 A-AATAAAATAAAATTAAAAT
3089492 AAATAAA
1 AAATAAA
3089499 CCTAGATTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 5 0.22
20 12 0.52
21 6 0.26
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
AAATAAAATAAAATTAAAAT
Found at i:3092204 original size:22 final size:22
Alignment explanation
Indices: 3092174--3092215 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3092164 ACAGAATTCC
3092174 ATTTGTAATT-TATAAGTTAACA
1 ATTTGTAATTATATAA-TTAACA
*
3092196 ATTTTTAATTATATAATTAA
1 ATTTGTAATTATATAATTAA
3092216 AAATACATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (22 bp):
ATTTGTAATTATATAATTAACA
Found at i:3094140 original size:3 final size:3
Alignment explanation
Indices: 3094132--3095692 Score: 1436
Period size: 3 Copynumber: 535.0 Consensus size: 3
3094122 CAAACTCTTA
3094132 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC- TCT TCT TC- TCT TCT T-T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
3094177 TC- TCT TC- TCT T-T TCCT TCT TC- TCT TCT TC- TCTT TCT CTCT TCT
1 TCT TCT TCT TCT TCT T-CT TCT TCT TCT TCT TCT TC-T TCT -TCT TCT
3094220 TCT TC- TCT TC- TCT TCT TCT TC- TCT TCT TCT TC- TCT TCT TCT T-T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* *
3094263 TCT TCT CCT TCT TC- TCTT TCT T-T CCT TCT TCT TC- TCT TCT TCT
1 TCT TCT TCT TCT TCT TC-T TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
3094306 TCT TCT TCT TCCT TCT TCT TCT TCT TCT CCT TCT TCT TCT CTCTT TCT
1 TCT TCT TCT T-CT TCT TCT TCT TCT TCT TCT TCT TCT TCT -TC-T TCT
*
3094354 T-T T-T TCT TTT TCCT TCT CTCT TCT T-T TCTT TCT TCT T-T TCT TCT
1 TCT TCT TCT TCT T-CT TCT -TCT TCT TCT TC-T TCT TCT TCT TCT TCT
* * *
3094398 TCT CCT TTT TCT TC- TCTT TCT TCT TCT TC- TCT CCT TCT TCTT TCT
1 TCT TCT TCT TCT TCT TC-T TCT TCT TCT TCT TCT TCT TCT TC-T TCT
3094443 TCT TC- TCT TCT TCT T-T CTCT T-T TC- TCT TC- TCT TC- TCT TCT
1 TCT TCT TCT TCT TCT TCT -TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * *
3094483 TTT TCT TCT TCT T-T CTCT TCT CCT TCT TC- TCT TTT TCT TC- TCT
1 TCT TCT TCT TCT TCT -TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
3094526 TCT T-T TCCT TCT TCT TC- TCT TCT TCT TCT T-T TCT TCT TCT CCT
1 TCT TCT T-CT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
3094569 T-T TCT TCT CCT TCT TCT TC- TCT TCT T-T CTCT T-T TCTT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT -TCT TCT TC-T TCT TCT
3094612 TCT TC- TCT TCT TCT TC- TCT TCT TCT TC- TCT TCT TCT TCCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T-CT TCT
3094655 TCT TCT TCCT TCT TCT TCT TCT TC- TCT TCT TCTT TCT TCT TCT TCT
1 TCT TCT T-CT TCT TCT TCT TCT TCT TCT TCT TC-T TCT TCT TCT TCT
*
3094701 TCT TCT TC- TCT TCT TCT TC- TCTT TCTT TCT TCT TCT TCT TTT TCT
1 TCT TCT TCT TCT TCT TCT TCT TC-T TC-T TCT TCT TCT TCT TCT TCT
3094746 TC- TCT TCT TCT TC- TCT TCT TCT TCT TCT TCT TCTT TCT TCT TC-
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC-T TCT TCT TCT
* *
3094789 TCT TCT T-T TC- TCT TC- TCT TCT TTT TCT CCTT TCT TC- TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC-T TCT TCT TCT TCT
*
3094831 TCT TCT CCT TCT TCT TCT TCT TCT TC- TCT TC- TCT TC- TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
3094876 T-T TCT TCT TCT CTCT TCT TCT TCT TCT TCT TCT TCT TCTT TCT TCT
1 TCT TCT TCT TCT -TCT TCT TCT TCT TCT TCT TCT TCT TC-T TCT TCT
*
3094922 TCT TCT TCT TCT TCG TCTT TCT TCT TCT T-T TCT TCT TCT TC- TCT
1 TCT TCT TCT TCT TCT TC-T TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
3094966 T-T TCT TCT TCT TCT TCT TCT T-T TCT TCT TCT TCT TCT T-G TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
3095011 TCT TC- TCT TC- TCT TCCT TCTT TCT TCT TCT TC- TCTT TCT TC- TCC
1 TCT TCT TCT TCT TCT T-CT TC-T TCT TCT TCT TCT TC-T TCT TCT TCT
* * * * * *
3095055 TCT TC- TCC TCT TCCT CCT TCCT CCT TCC TC- TCT TCT TCC TCC TCT
1 TCT TCT TCT TCT T-CT TCT T-CT TCT TCT TCT TCT TCT TCT TCT TCT
* * * * *
3095100 TCT TCT TCT TCC TC- TCT TC- TCT TCT CCT TCC T-T TCT TCC TCT TCC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * *
3095145 T-T TCT TCTT TCT TC- TCT TCT TCCT TCT TCC TCT TC- TCC TCT TCC
1 TCT TCT TC-T TCT TCT TCT TCT T-CT TCT TCT TCT TCT TCT TCT TCT
* * * *
3095189 TCT TC- TCT TCC TCTT TCT TC- CCT TC- TCT CTCT TCC TCT TCC TCT
1 TCT TCT TCT TCT TC-T TCT TCT TCT TCT TCT -TCT TCT TCT TCT TCT
* * * * * * *
3095233 TCC TCT TCC TCT TCC TCT TCCT TCC TCT TCC TCT TCC T-T TCC TCT
1 TCT TCT TCT TCT TCT TCT T-CT TCT TCT TCT TCT TCT TCT TCT TCT
* * * * * * *
3095278 TC- TCT TCC TCT TCC T-T TC- TCT TCC TCC TCC TCT TCT TCC TCC TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * * * * *
3095323 TCC TCT TCCT TCC T-T TCC TCC TCC TCT TCT CTCT TC- CCT TCT CTCT
1 TCT TCT T-CT TCT TCT TCT TCT TCT TCT TCT -TCT TCT TCT TCT -TCT
* * * *
3095369 TCT TCC TCT TCT TCC TCT TCT TCC TCT TCT TCT TCT TCC TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
3095417 TCT TC- TCT TCT TCC TCT TCT TCT TCT TC- TCT TCT TC- TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * * * * * *
3095462 TCC TCT TCT TCC TCT TCT TCC TCT TCT TCC TCC TCT TCA TCT TCT TCC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * * * *
3095510 TCT TCT TCC TCT TCT TCC TCT TCT TCT TCT TCC TCT TCT TCT TCC TCA
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * *
3095558 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT ACC TCC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * * *
3095606 TCC TCC TCC TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCC TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
3095654 TCT TCT TCT TCT TCT TCT TCC TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
3095693 AATCTAATAA
Statistics
Matches: 1300, Mismatches: 136, Indels: 244
0.77 0.08 0.15
Matches are distributed among these distances:
2 156 0.12
3 1043 0.80
4 100 0.08
5 1 0.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:3097110 original size:22 final size:21
Alignment explanation
Indices: 3097070--3097116 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
3097060 ATGCACATCT
* *
3097070 TGAAATTTTATATTCTCCACC
1 TGAAATTTTATAGTATCCACC
*
3097091 ATGAAATTTTATCGTATCCACC
1 -TGAAATTTTATAGTATCCACC
3097113 TGAA
1 TGAA
3097117 TATAAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.38
Consensus pattern (21 bp):
TGAAATTTTATAGTATCCACC
Found at i:3108892 original size:2 final size:2
Alignment explanation
Indices: 3108885--3108910 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3108875 TAAATAATTA
3108885 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3108911 GCAATAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3110894 original size:27 final size:27
Alignment explanation
Indices: 3110864--3110937 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 27
3110854 TAAAGGACGC
3110864 ATGCCAAACCATGGTGATCAACA-ACCT
1 ATGCCAAACCATGGTGATCAA-ATACCT
* * *
3110891 ATGCCAACCCATGGAGATGAAATACCT
1 ATGCCAAACCATGGTGATCAAATACCT
3110918 ATGCCACCAAACCATGGTGA
1 ATG---CCAAACCATGGTGA
3110938 ATGTGTAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
26 1 0.03
27 25 0.66
30 12 0.32
ACGTcount: A:0.36, C:0.28, G:0.18, T:0.18
Consensus pattern (27 bp):
ATGCCAAACCATGGTGATCAAATACCT
Found at i:3117941 original size:28 final size:27
Alignment explanation
Indices: 3117893--3118020 Score: 80
Period size: 29 Copynumber: 4.4 Consensus size: 27
3117883 AAAATTAAAG
* *
3117893 AATATATTTTATATATCTTAAATT-TTAA
1 AATATATTTTAT-TTTTTTAAATTATT-A
* * *
3117921 AATTATCTTTTGTTTTTTTAACTTATTA
1 AA-TATATTTTATTTTTTTAAATTATTA
*
3117949 AATATATTTTATTTTTTTCTTAACTTATTA
1 AATATATTTTA--TTTTT-TTAAATTATTA
**
3117979 AATATA-TTTATTATTATTTAAATGTAAAA
1 AATATATTTTATT-TT-TTTAAAT-TATTA
3118008 ATATATATTTTAT
1 A-ATATATTTTAT
3118021 CTTTATCATC
Statistics
Matches: 80, Mismatches: 10, Indels: 17
0.75 0.09 0.16
Matches are distributed among these distances:
27 9 0.11
28 20 0.25
29 24 0.30
30 22 0.28
31 5 0.06
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.58
Consensus pattern (27 bp):
AATATATTTTATTTTTTTAAATTATTA
Found at i:3117974 original size:30 final size:28
Alignment explanation
Indices: 3117933--3118173 Score: 128
Period size: 29 Copynumber: 8.0 Consensus size: 28
3117923 TTATCTTTTG
*
3117933 TTTTTTTAACTTATTAAATATATTTTATT
1 TTTTTTTAACTTA-AAAATATATTTTATT
*
3117962 TTTTTCTTAACTTATTAAATATA-TTTATT
1 TTTTT-TTAACTTA-AAAATATATTTTATT
* * *
3117991 ATTATTTAAATGTAAAAATATATATTTTATCT
1 TTTTTTTAACT-T-AAAA-ATATATTTTAT-T
* ** *
3118023 TTATCATCACTTAAAAAATATATTTT-TT
1 TTTTTTTAACTT-AAAAATATATTTTATT
* * *
3118051 AAAATATGTTAACTT-AAAATATATTTAAATATTTT
1 ---TTTTTTTAACTTAAAAATATATTT---TA--TT
*
3118086 ATTCTTATCTTCACTTAAAAATATATTTTATT
1 -TT-TT-T-TTAACTTAAAAATATATTTTATT
* *
3118118 TTATTTTAAATTAAAAATATATTTTATT
1 TTTTTTTAACTTAAAAATATATTTTATT
*
3118146 TTTATTTTAAATTAAAAATATATTTTAT
1 TTT-TTTTAACTTAAAAATATATTTTAT
3118174 CATTATCTAA
Statistics
Matches: 169, Mismatches: 23, Indels: 40
0.73 0.10 0.17
Matches are distributed among these distances:
28 29 0.17
29 54 0.32
30 33 0.20
31 21 0.12
32 8 0.05
33 2 0.01
34 3 0.02
35 2 0.01
36 6 0.04
37 11 0.07
ACGTcount: A:0.39, C:0.05, G:0.01, T:0.55
Consensus pattern (28 bp):
TTTTTTTAACTTAAAAATATATTTTATT
Found at i:3118113 original size:29 final size:29
Alignment explanation
Indices: 3118079--3118197 Score: 143
Period size: 29 Copynumber: 4.1 Consensus size: 29
3118069 ATATATTTAA
* *
3118079 ATATTTTATTCTTATCTTCACTTAAAAAT
1 ATATTTTATTCTTATCTTAAATTAAAAAT
*
3118108 ATATTTTATT-TTATTTTAAATTAAAAAT
1 ATATTTTATTCTTATCTTAAATTAAAAAT
* *
3118136 ATATTTTATTTTTATTTTAAATTAAAAAT
1 ATATTTTATTCTTATCTTAAATTAAAAAT
*
3118165 ATATTTTA-TCATTATCTAAAATTTTAAAAAT
1 ATATTTTATTC-TTATCTTAAA--TTAAAAAT
3118196 AT
1 AT
3118198 CTTAACTTAA
Statistics
Matches: 80, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
28 26 0.32
29 44 0.55
31 10 0.12
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (29 bp):
ATATTTTATTCTTATCTTAAATTAAAAAT
Found at i:3118132 original size:28 final size:28
Alignment explanation
Indices: 3118079--3118173 Score: 145
Period size: 29 Copynumber: 3.3 Consensus size: 28
3118069 ATATATTTAA
* * *
3118079 ATATTTTATTCTTATCTTCACTTAAAAAT
1 ATATTTTATT-TTATTTTAAATTAAAAAT
3118108 ATATTTTATTTTATTTTAAATTAAAAAT
1 ATATTTTATTTTATTTTAAATTAAAAAT
3118136 ATATTTTATTTTTATTTTAAATTAAAAAT
1 ATATTTTA-TTTTATTTTAAATTAAAAAT
3118165 ATATTTTAT
1 ATATTTTAT
3118174 CATTATCTAA
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
28 24 0.39
29 38 0.61
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (28 bp):
ATATTTTATTTTATTTTAAATTAAAAAT
Found at i:3118225 original size:18 final size:17
Alignment explanation
Indices: 3118187--3118229 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
3118177 TATCTAAAAT
3118187 TTTAAAAA-TATCTTAA
1 TTTAAAAATTATCTTAA
* *
3118203 CTTAAAAATGTATTTTAA
1 TTTAAAAAT-TATCTTAA
3118221 TTTAAAAAT
1 TTTAAAAAT
3118230 AAAATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 7 0.32
18 15 0.68
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (17 bp):
TTTAAAAATTATCTTAA
Found at i:3118275 original size:32 final size:33
Alignment explanation
Indices: 3118220--3118286 Score: 91
Period size: 32 Copynumber: 2.0 Consensus size: 33
3118210 ATGTATTTTA
* *
3118220 ATTTAAAAATAAAATATAATTT-AAGTTAAGAT
1 ATTTAAAAAAAAAAGATAATTTAAAGTTAAGAT
*
3118252 ATTTAAAAAAAAAAGATATTTTAAAAGTTAAGAT
1 ATTTAAAAAAAAAAGATAATTT-AAAGTTAAGAT
3118286 A
1 A
3118287 ATGATAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 19 0.63
34 11 0.37
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.34
Consensus pattern (33 bp):
ATTTAAAAAAAAAAGATAATTTAAAGTTAAGAT
Found at i:3118284 original size:17 final size:17
Alignment explanation
Indices: 3118242--3118286 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
3118232 AATATAATTT
3118242 AAGTTAAGATATTTAAA
1 AAGTTAAGATATTTAAA
*** *
3118259 AAAAAAAGATATTTTAA
1 AAGTTAAGATATTTAAA
3118276 AAGTTAAGATA
1 AAGTTAAGATA
3118287 ATGATAATAA
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.11, T:0.31
Consensus pattern (17 bp):
AAGTTAAGATATTTAAA
Found at i:3118401 original size:30 final size:29
Alignment explanation
Indices: 3118367--3118460 Score: 79
Period size: 28 Copynumber: 3.2 Consensus size: 29
3118357 TGTCAAATAA
3118367 ATTTTAACTGATGATAAATATAAAATATAT
1 ATTTTAA-TGATGATAAATATAAAATATAT
* *
3118397 ATTTTAA-G-TTA-AAATATTTTAAATATAT
1 ATTTTAATGATGATAAATA--TAAAATATAT
*
3118425 ATTTTTAAGTGATGATAAAGT-TAAAACATAT
1 A-TTTTAA-TGATGATAAA-TATAAAATATAT
3118456 ATTTT
1 ATTTT
3118461 TACTTTAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
26 5 0.10
27 2 0.04
28 11 0.22
29 6 0.12
30 11 0.22
31 10 0.20
32 2 0.04
33 3 0.06
34 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.45
Consensus pattern (29 bp):
ATTTTAATGATGATAAATATAAAATATAT
Found at i:3118502 original size:26 final size:28
Alignment explanation
Indices: 3118472--3118582 Score: 82
Period size: 31 Copynumber: 3.7 Consensus size: 28
3118462 ACTTTAAAAT
3118472 AAAAAT-AAATATATTTAATAAGTTAAG
1 AAAAATAAAATATATTTAATAAGTTAAG
*
3118499 AAAAAAAATAAAATATATTTAATAAGTTAAAACA
1 ---AAAAATAAAATATATTTAATAAGTT--AA-G
* *
3118533 AAAAATAAAAGATAATTTTAA-AATTTAAG
1 AAAAATAAAATAT-A-TTTAATAAGTTAAG
* *
3118562 ATATATAAAATATTATTTAAT
1 AAAAATAAAATA-TATTTAAT
3118583 TTTGAGTAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 17
0.73 0.08 0.19
Matches are distributed among these distances:
28 5 0.08
29 10 0.15
30 9 0.14
31 30 0.45
32 5 0.08
33 7 0.11
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.33
Consensus pattern (28 bp):
AAAAATAAAATATATTTAATAAGTTAAG
Found at i:3118516 original size:31 final size:31
Alignment explanation
Indices: 3118472--3118542 Score: 119
Period size: 31 Copynumber: 2.3 Consensus size: 31
3118462 ACTTTAAAAT
3118472 AAAAAT-AAATATATTTAATAAGTTAAGAA-A
1 AAAAATAAAATATATTTAATAAGTTAA-AACA
3118502 AAAAATAAAATATATTTAATAAGTTAAAACA
1 AAAAATAAAATATATTTAATAAGTTAAAACA
3118533 AAAAATAAAA
1 AAAAATAAAA
3118543 GATAATTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
30 8 0.21
31 31 0.79
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.27
Consensus pattern (31 bp):
AAAAATAAAATATATTTAATAAGTTAAAACA
Found at i:3121262 original size:2 final size:2
Alignment explanation
Indices: 3121255--3121283 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3121245 TAAGTAAGAT
3121255 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3121284 GTGTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3125351 original size:11 final size:11
Alignment explanation
Indices: 3125335--3125397 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
3125325 AAAATTACAT
3125335 TATTAAAAATA
1 TATTAAAAATA
3125346 TATTAAAAATA
1 TATTAAAAATA
* * ***
3125357 CACTATTGATA
1 TATTAAAAATA
3125368 -ATTATAAAAT-
1 TATTA-AAAATA
3125378 T-TTAAAAATA
1 TATTAAAAATA
3125388 TATTAAAAAT
1 TATTAAAAAT
3125398 TCTATAATAC
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 5 0.13
10 7 0.18
11 27 0.69
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:3134525 original size:3 final size:3
Alignment explanation
Indices: 3134517--3134614 Score: 178
Period size: 3 Copynumber: 32.7 Consensus size: 3
3134507 TTAATATATT
*
3134517 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
3134565 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3134613 TA
1 TA
3134615 TGGATAAAAA
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 91 1.00
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3135074 original size:113 final size:113
Alignment explanation
Indices: 3134933--3135571 Score: 981
Period size: 113 Copynumber: 5.6 Consensus size: 113
3134923 AGAATTATGC
* * * * *
3134933 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTATCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
3134998 TATGAACTTTCTCTGGAAAGGCTGATCCATCAAATGATGGACTCAGGT
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGGATTCAGGT
*
3135046 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
3135111 TATGAACTTTCTCTGGAAAAGATAATCCATTAATTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGGATTCAGGT
3135159 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * *
3135224 TATGATCTTTCTCTGGAAAGGCTGATCCATCAAATGATGGACTCAGGT
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGGATTCAGGT
3135272 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * ***
3135337 TATGAACCTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTCAAAC
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGGATTCAGGT
* *
3135385 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCATATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * **
3135450 TATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATAGATTTAAGCA
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGGA-TTCAGGT
3135499 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
3135564 TATGAACT
66 TATGAACT
3135572 CGAACTGGAA
Statistics
Matches: 480, Mismatches: 45, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
113 406 0.85
114 74 0.15
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGGATTCAGGT
Found at i:3135437 original size:24 final size:23
Alignment explanation
Indices: 3135402--3135446 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
3135392 TGAACAAATT
*
3135402 CTTCTCATTATGAATTTCTTCTTC
1 CTTCTCATTATG-AGTTCTTCTTC
3135426 CTTCTTCA-TATGAGTTCTTCT
1 CTTC-TCATTATGAGTTCTTCT
3135447 CATTATGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 8 0.42
25 3 0.16
ACGTcount: A:0.16, C:0.24, G:0.07, T:0.53
Consensus pattern (23 bp):
CTTCTCATTATGAGTTCTTCTTC
Found at i:3136606 original size:84 final size:84
Alignment explanation
Indices: 3136187--3136616 Score: 700
Period size: 84 Copynumber: 5.1 Consensus size: 84
3136177 GTAATTTTTA
*
3136187 CCAAACCAGATCAAATAACTCAAAGAATACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTA
1 CCAAACCAGATCAGATAACTCAAAGAATACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTA
* *
3136252 AATTCAATGATTGGTTTTA
66 AATTCAATGATTGGTTCTG
* * *
3136271 CCAAACCAAATCAGATAATTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTA
1 CCAAACCAGATCAGATAACTCAAAGAATACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTA
*
3136336 AATTCAATGATTGGTTCCG
66 AATTCAATGATTGGTTCTG
*
3136355 TCC-AACCAGATCAGATAACTCAAAGAATACTTCCAGAAGATTCTATTGAGCACATTCATCTTCT
1 -CCAAACCAGATCAGATAACTCAAAGAATACTTCCAGAAGATGCTATTGAGCACATTCATCTTCT
*
3136419 AAATTCAATGATTGGTTCCG
65 AAATTCAATGATTGGTTCTG
* * * *
3136439 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCA
1 CCAAACCAGATCAGATAACTCAAAGAATACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTA
3136504 AATTCAATGATTGGTTCTG
66 AATTCAATGATTGGTTCTG
*
3136523 CCAAATCAGATCAGATAACTCAAAGAATACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTA
1 CCAAACCAGATCAGATAACTCAAAGAATACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTA
3136588 AATTCAATGATTGGTTCTG
66 AATTCAATGATTGGTTCTG
* *
3136607 CTAAATCAGA
1 CCAAACCAGA
3136617 ACACTTATTT
Statistics
Matches: 323, Mismatches: 21, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
83 2 0.01
84 319 0.99
85 2 0.01
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (84 bp):
CCAAACCAGATCAGATAACTCAAAGAATACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTA
AATTCAATGATTGGTTCTG
Found at i:3137737 original size:14 final size:15
Alignment explanation
Indices: 3137718--3137746 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3137708 ACCTTGACCC
3137718 CCTTTTT-CTTTTTT
1 CCTTTTTCCTTTTTT
3137732 CCTTTTTCCTTTTTT
1 CCTTTTTCCTTTTTT
3137747 TTTCAAGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (15 bp):
CCTTTTTCCTTTTTT
Found at i:3145027 original size:14 final size:15
Alignment explanation
Indices: 3145008--3145039 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3144998 TATTTTTTCA
3145008 AATTTTAA-TTAATG
1 AATTTTAACTTAATG
3145022 AATTTTAACTTAATG
1 AATTTTAACTTAATG
3145037 AAT
1 AAT
3145040 AAAATAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (15 bp):
AATTTTAACTTAATG
Found at i:3148422 original size:18 final size:17
Alignment explanation
Indices: 3148374--3148424 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
3148364 AAATACTTGC
*
3148374 AAATAAAATAAAACATAT
1 AAAT-AAATAAAAAATAT
*
3148392 AAAT-ATTATAAAAATAAT
1 AAATAAATA-AAAAAT-AT
3148410 AAATAAATAAAAAAT
1 AAATAAATAAAAAAT
3148425 TTGAAAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
16 3 0.11
17 5 0.19
18 16 0.59
19 3 0.11
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATAAATAAAAAATAT
Found at i:3150579 original size:3 final size:3
Alignment explanation
Indices: 3150571--3150638 Score: 109
Period size: 3 Copynumber: 22.7 Consensus size: 3
3150561 TTAATATATT
* *
3150571 TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
3150619 TAA TAA TAT TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
3150639 TGGATAAAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:3151638 original size:2 final size:2
Alignment explanation
Indices: 3151625--3151655 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3151615 CAAACGATAA
*
3151625 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3151656 AGCCCATCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3159987 original size:21 final size:21
Alignment explanation
Indices: 3159854--3160000 Score: 105
Period size: 21 Copynumber: 6.9 Consensus size: 21
3159844 TCGAGGGTTC
3159854 TATGTGGTCCTTCGGGACATA
1 TATGTGGTCCTTCGGGACATA
** * *
3159875 TATGTAATCCTTTGGAACATA
1 TATGTGGTCCTTCGGGACATA
* * * * * *
3159896 TATGCGGTTCTTTGAGATACA
1 TATGTGGTCCTTCGGGACATA
* * * * *
3159917 TATTTGGTCATTTGGAATATA
1 TATGTGGTCCTTCGGGACATA
* ** *
3159938 TATGTGGTCCTTAAGGAGATTTC
1 TATGTGGTCCTT-CGG-GACATA
3159961 TATGTGGTCCTTCGGGACATA
1 TATGTGGTCCTTCGGGACATA
3159982 TATGTGGTCCTTCGGGACA
1 TATGTGGTCCTTCGGGACA
3160001 AATTCTATAT
Statistics
Matches: 95, Mismatches: 29, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
21 76 0.80
22 4 0.04
23 15 0.16
ACGTcount: A:0.23, C:0.15, G:0.24, T:0.37
Consensus pattern (21 bp):
TATGTGGTCCTTCGGGACATA
Found at i:3160677 original size:16 final size:17
Alignment explanation
Indices: 3160650--3160683 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3160640 ATTTCCATTA
3160650 TTTTGTAAAAGTAAATG
1 TTTTGTAAAAGTAAATG
*
3160667 TTTTG-AAAAGTTAATG
1 TTTTGTAAAAGTAAATG
3160683 T
1 T
3160684 AACACCTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (17 bp):
TTTTGTAAAAGTAAATG
Found at i:3162881 original size:23 final size:26
Alignment explanation
Indices: 3162805--3162870 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 26
3162795 TTTTTAGTTT
* *
3162805 AATAATA-TATAATAAATTATTAATAAA
1 AATAATATTATTATTAATT-TT-ATAAA
*
3162832 ACTAATATTATTTATTAATTTTATAAA
1 AATAATATTA-TTATTAATTTTATAAA
3162859 AATAATATTATT
1 AATAATATTATT
3162871 TAATTTCTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
26 2 0.06
27 20 0.61
28 4 0.12
29 7 0.21
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (26 bp):
AATAATATTATTATTAATTTTATAAA
Found at i:3162932 original size:24 final size:24
Alignment explanation
Indices: 3162780--3162933 Score: 61
Period size: 24 Copynumber: 6.2 Consensus size: 24
3162770 GATAATTTTA
*
3162780 TAATATAATATAATATTTTTAGTT
1 TAATATAATATAATATTTTTATTT
**
3162804 TAATA-ATATATAATA-AATTA--T
1 TAATATA-ATATAATATTTTTATTT
* *
3162825 TAATAAAACTAATATTATTTATTAATTT
1 TAATATAA-T-ATAATATTT-TT-ATTT
*
3162853 T-ATA-AAAATAATATTATTTAATTT
1 TAATATAATATAATATT-TTT-ATTT
* ** *
3162877 CTAAATATTTAAAAT-ATATTTTCCTTA
1 -T-AATA--TAATATAATATTTTTATTT
*
3162904 AAATATAATATAATATTTTTATTT
1 TAATATAATATAATATTTTTATTT
3162928 TAATAT
1 TAATAT
3162934 TATAAATTTT
Statistics
Matches: 97, Mismatches: 16, Indels: 34
0.66 0.11 0.23
Matches are distributed among these distances:
21 7 0.07
22 2 0.02
23 14 0.14
24 41 0.42
25 8 0.08
26 3 0.03
27 8 0.08
28 4 0.04
29 5 0.05
30 5 0.05
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.50
Consensus pattern (24 bp):
TAATATAATATAATATTTTTATTT
Found at i:3163057 original size:30 final size:32
Alignment explanation
Indices: 3163023--3163082 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 32
3163013 TAAGTATTTA
3163023 ATATAAT-TA-TAATATTTTTATTTAAAAAAT
1 ATATAATATACTAATATTTTTATTTAAAAAAT
*
3163053 ATATAATAATACTGATATTTTTATTTAAAA
1 ATATAAT-ATACTAATATTTTTATTTAAAA
3163083 TTGTAGATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 7 0.27
32 2 0.08
33 17 0.65
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (32 bp):
ATATAATATACTAATATTTTTATTTAAAAAAT
Found at i:3163990 original size:31 final size:31
Alignment explanation
Indices: 3163950--3164022 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
3163940 TTTGTACACT
* *
3163950 TTTGCTCACTTACATTATCATTTTATTAAGA
1 TTTGGTCACTTACATTATAATTTTATTAAGA
* *
3163981 TTTGGTCACTTACGTTATAATTTTATTAAGT
1 TTTGGTCACTTACATTATAATTTTATTAAGA
*
3164012 TTTGGTTACTT
1 TTTGGTCACTT
3164023 GGACGTTGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.25, C:0.12, G:0.11, T:0.52
Consensus pattern (31 bp):
TTTGGTCACTTACATTATAATTTTATTAAGA
Found at i:3165272 original size:12 final size:12
Alignment explanation
Indices: 3165255--3165279 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3165245 CGAACACGTA
3165255 CATTTCTATTAT
1 CATTTCTATTAT
3165267 CATTTCTATTAT
1 CATTTCTATTAT
3165279 C
1 C
3165280 TAAGTTAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.20, G:0.00, T:0.56
Consensus pattern (12 bp):
CATTTCTATTAT
Found at i:3168883 original size:57 final size:57
Alignment explanation
Indices: 3168815--3168933 Score: 238
Period size: 57 Copynumber: 2.1 Consensus size: 57
3168805 TCCCACCAAT
3168815 AAAAATGGCTGTAAAAAATACCCGAATATATTATATAAAATTTATTAAAGAATTAAA
1 AAAAATGGCTGTAAAAAATACCCGAATATATTATATAAAATTTATTAAAGAATTAAA
3168872 AAAAATGGCTGTAAAAAATACCCGAATATATTATATAAAATTTATTAAAGAATTAAA
1 AAAAATGGCTGTAAAAAATACCCGAATATATTATATAAAATTTATTAAAGAATTAAA
3168929 AAAAA
1 AAAAA
3168934 ATAGGTGTCC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 62 1.00
ACGTcount: A:0.56, C:0.07, G:0.08, T:0.29
Consensus pattern (57 bp):
AAAAATGGCTGTAAAAAATACCCGAATATATTATATAAAATTTATTAAAGAATTAAA
Found at i:3171677 original size:71 final size:71
Alignment explanation
Indices: 3171555--3171698 Score: 225
Period size: 71 Copynumber: 2.0 Consensus size: 71
3171545 AAACTAATTT
* * * *
3171555 TAAAGAGTTGAAAGAAAATTGTTTCGAGAACGAGGCAAAATCATTTGCCCGGGTATACATATTAC
1 TAAAGAGTTGAAAGAAAATTGTTCCAAGAACGAGGCAAAATAATTTGCCCGGGCATACATATTAC
3171620 AAATCA
66 AAATCA
* * *
3171626 TAAAGAGTTTAAAGAAAATTGTTCCAAGAACGAGGTAAAATAATTTTCCCGGGCATACATATTAC
1 TAAAGAGTTGAAAGAAAATTGTTCCAAGAACGAGGCAAAATAATTTGCCCGGGCATACATATTAC
3171691 AAATCA
66 AAATCA
3171697 TA
1 TA
3171699 GGAGGGATAT
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 66 1.00
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.26
Consensus pattern (71 bp):
TAAAGAGTTGAAAGAAAATTGTTCCAAGAACGAGGCAAAATAATTTGCCCGGGCATACATATTAC
AAATCA
Found at i:3173692 original size:24 final size:24
Alignment explanation
Indices: 3173665--3173770 Score: 110
Period size: 24 Copynumber: 4.5 Consensus size: 24
3173655 GTAAACGGAT
*
3173665 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
3173689 ATATCAGATATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTC
*
3173713 ATATCAG-AATCAGAATAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* * *
3173736 AGATAACG-AATCAGAACATAATTC
1 ATATCA-GAAATCAGAACAGAATTC
3173760 A-ATTCAGAAAT
1 ATA-TCAGAAAT
3173771 AAGATAAAAT
Statistics
Matches: 68, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
23 19 0.28
24 49 0.72
ACGTcount: A:0.50, C:0.16, G:0.11, T:0.23
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATTC
Found at i:3176228 original size:13 final size:13
Alignment explanation
Indices: 3176206--3176247 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
3176196 CGGTCAACGT
*
3176206 GTCAAAGGGTCGG
1 GTCAACGGGTCGG
*
3176219 GTCAACGGGTCGT
1 GTCAACGGGTCGG
*
3176232 GTCAACAGGTCGG
1 GTCAACGGGTCGG
3176245 GTC
1 GTC
3176248 GGGTTATGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.19, C:0.21, G:0.40, T:0.19
Consensus pattern (13 bp):
GTCAACGGGTCGG
Found at i:3178361 original size:12 final size:11
Alignment explanation
Indices: 3178326--3178410 Score: 55
Period size: 12 Copynumber: 7.3 Consensus size: 11
3178316 AGATATCAGA
*
3178326 AATCAAAACAG
1 AATCAGAACAG
* *
3178337 AATTCATATCAG
1 AA-TCAGAACAG
3178349 ATATCAGAACAG
1 A-ATCAGAACAG
*
3178361 AATCCAGATCAG
1 AAT-CAGAACAG
*
3178373 AATCAGAAAAG
1 AATCAGAACAG
3178384 AATTCAGATA-ACG
1 AA-TCAGA-ACA-G
*
3178397 TATCAGAACAG
1 AATCAGAACAG
3178408 AAT
1 AAT
3178411 TCAATTCGGA
Statistics
Matches: 58, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
11 16 0.28
12 38 0.66
13 4 0.07
ACGTcount: A:0.51, C:0.16, G:0.14, T:0.19
Consensus pattern (11 bp):
AATCAGAACAG
Found at i:3178401 original size:47 final size:48
Alignment explanation
Indices: 3178320--3178410 Score: 125
Period size: 47 Copynumber: 1.9 Consensus size: 48
3178310 AAACGGAGAT
* *
3178320 ATCAGAAATCAAAACAGAATTCATATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAGATAAGATATCAGAACAGAATCCAG
3178368 ATCAG-AATCAGAAA-AGAATTCAGATAACG-TATCAGAACAGAAT
1 ATCAGAAATCA-AAACAGAATTCAGATAA-GATATCAGAACAGAAT
3178411 TCAATTCGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
47 30 0.77
48 9 0.23
ACGTcount: A:0.51, C:0.16, G:0.14, T:0.19
Consensus pattern (48 bp):
ATCAGAAATCAAAACAGAATTCAGATAAGATATCAGAACAGAATCCAG
Found at i:3178409 original size:24 final size:23
Alignment explanation
Indices: 3178327--3178413 Score: 102
Period size: 24 Copynumber: 3.7 Consensus size: 23
3178317 GATATCAGAA
* *
3178327 ATCAAAACAGAATTCATATCAGAT
1 ATCAGAACAGAATTCAGATCAG-T
* *
3178351 ATCAGAACAGAATCCAGATCAGA
1 ATCAGAACAGAATTCAGATCAGT
* *
3178374 ATCAGAAAAGAATTCAGATAACGT
1 ATCAGAACAGAATTCAGATCA-GT
3178398 ATCAGAACAGAATTCA
1 ATCAGAACAGAATTCA
3178414 ATTCGGAAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 18 0.34
24 35 0.66
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.20
Consensus pattern (23 bp):
ATCAGAACAGAATTCAGATCAGT
Found at i:3178425 original size:24 final size:26
Alignment explanation
Indices: 3178316--3178427 Score: 98
Period size: 24 Copynumber: 4.7 Consensus size: 26
3178306 CGGTAAACGG
*
3178316 AGATATCAGAAATCAAAACAGAATTC
1 AGATATCAGAAATCAGAACAGAATTC
* *
3178342 --ATATCAGATATCAGAACAGAATCC
1 AGATATCAGAAATCAGAACAGAATTC
*
3178366 AG--ATCAG-AATCAGAAAAGAATTC
1 AGATATCAGAAATCAGAACAGAATTC
* *
3178389 AGATAAC-G-TATCAGAACAGAATTC
1 AGATATCAGAAATCAGAACAGAATTC
*
3178413 A-AT-TCGGAAATCAGA
1 AGATATCAGAAATCAGA
3178428 TAAAATATTT
Statistics
Matches: 69, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
22 1 0.01
23 18 0.26
24 48 0.70
25 2 0.03
ACGTcount: A:0.49, C:0.16, G:0.15, T:0.20
Consensus pattern (26 bp):
AGATATCAGAAATCAGAACAGAATTC
Found at i:3180863 original size:13 final size:13
Alignment explanation
Indices: 3180845--3180889 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
3180835 CAACGGTCAA
3180845 CGGGTCAAAGGGT
1 CGGGTCAAAGGGT
* *
3180858 CGGGTCAACGTGT
1 CGGGTCAAAGGGT
3180871 CGGGTCAACA-GGT
1 CGGGTCAA-AGGGT
3180884 CGGGTC
1 CGGGTC
3180890 GGGTAAACGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.18, C:0.22, G:0.42, T:0.18
Consensus pattern (13 bp):
CGGGTCAAAGGGT
Found at i:3180890 original size:18 final size:18
Alignment explanation
Indices: 3180869--3180911 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
3180859 GGGTCAACGT
*
3180869 GTCGGGTCAAC-AGGTCGG
1 GTCGGGTAAACGA-GTCGG
3180887 GTCGGGTAAACGAGTCGG
1 GTCGGGTAAACGAGTCGG
3180905 GTCGGGT
1 GTCGGGT
3180912 TATGACCGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 22 0.96
19 1 0.04
ACGTcount: A:0.16, C:0.19, G:0.47, T:0.19
Consensus pattern (18 bp):
GTCGGGTAAACGAGTCGG
Found at i:3183135 original size:21 final size:22
Alignment explanation
Indices: 3183111--3183178 Score: 59
Period size: 22 Copynumber: 3.0 Consensus size: 22
3183101 TAATATTTTA
*
3183111 ATTTTAATATAACCCTAAA-CT
1 ATTTTAAAATAACCCTAAACCT
*
3183132 ATTTAAAAAATAACCCTAAACCT
1 ATTT-TAAAATAACCCTAAACCT
* *
3183155 -TTTTAACAAAAAACCCTAACCCT
1 ATTTT-A-AAATAACCCTAAACCT
3183178 A
1 A
3183179 AACTATTCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
21 4 0.11
22 17 0.46
23 16 0.43
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (22 bp):
ATTTTAAAATAACCCTAAACCT
Found at i:3183145 original size:22 final size:24
Alignment explanation
Indices: 3183119--3183178 Score: 81
Period size: 23 Copynumber: 2.6 Consensus size: 24
3183109 TAATTTTAAT
3183119 ATAACCCTAAA-CTATTTAA-AAA
1 ATAACCCTAAACCTATTTAACAAA
*
3183141 ATAACCCTAAACCTTTTTAACAAA
1 ATAACCCTAAACCTATTTAACAAA
*
3183165 A-AACCCTAACCCTA
1 ATAACCCTAAACCTA
3183179 AACTATTCTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 11 0.33
23 18 0.55
24 4 0.12
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.25
Consensus pattern (24 bp):
ATAACCCTAAACCTATTTAACAAA
Found at i:3183828 original size:31 final size:31
Alignment explanation
Indices: 3183786--3183857 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 31
3183776 TTAAGTGCCT
*
3183786 AAAGTATTTTTTTGA-TCAAAATAAGTA-TC
1 AAAGTATTTTTTTAAGTCAAAATAAGTACTC
*
3183815 AAAAGTTATTTTTTTAAGTCAAAATAGGTACTC
1 -AAAG-TATTTTTTTAAGTCAAAATAAGTACTC
3183848 AAAGTATTTT
1 AAAGTATTTT
3183858 ATGTCAGGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
30 4 0.11
31 16 0.43
32 15 0.41
33 2 0.05
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.42
Consensus pattern (31 bp):
AAAGTATTTTTTTAAGTCAAAATAAGTACTC
Found at i:3184669 original size:14 final size:14
Alignment explanation
Indices: 3184652--3184679 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3184642 ATATATATAT
3184652 ATATATATAATGCA
1 ATATATATAATGCA
3184666 ATATATATAATGCA
1 ATATATATAATGCA
3184680 TGTGAACCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (14 bp):
ATATATATAATGCA
Found at i:3184674 original size:2 final size:2
Alignment explanation
Indices: 3184632--3184660 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3184622 AGTAAAAGTC
3184632 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3184661 ATGCAATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3185982 original size:15 final size:15
Alignment explanation
Indices: 3185962--3185993 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
3185952 TAGTACATTT
3185962 AAAGCTCATAACGTG
1 AAAGCTCATAACGTG
3185977 AAAGCTCATAACGTG
1 AAAGCTCATAACGTG
3185992 AA
1 AA
3185994 CCCTTTTGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.19
Consensus pattern (15 bp):
AAAGCTCATAACGTG
Found at i:3194888 original size:16 final size:16
Alignment explanation
Indices: 3194864--3194896 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3194854 TATCGCCGAC
*
3194864 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
3194880 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
3194896 C
1 C
3194897 ATGAATAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.33
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:3196425 original size:33 final size:33
Alignment explanation
Indices: 3196380--3196458 Score: 99
Period size: 33 Copynumber: 2.4 Consensus size: 33
3196370 CTCCAACTTT
*
3196380 GTTGGATAATGGTGACGTAGT-GGCTCCTGCTTC
1 GTTGGATGATGGTGACGTAGTGGGC-CCTGCTTC
* *
3196413 GTT-GATTGATGGTGATGTAGTGGGCCCTGCTTG
1 GTTGGA-TGATGGTGACGTAGTGGGCCCTGCTTC
3196446 GTTGGATGATGGT
1 GTTGGATGATGGT
3196459 TTGGAGCTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
32 2 0.05
33 33 0.82
34 5 0.12
ACGTcount: A:0.14, C:0.13, G:0.38, T:0.35
Consensus pattern (33 bp):
GTTGGATGATGGTGACGTAGTGGGCCCTGCTTC
Found at i:3200168 original size:20 final size:19
Alignment explanation
Indices: 3200134--3200172 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
3200124 AAGATTAGGT
3200134 GATTAAAATTTAAAGTTTA
1 GATTAAAATTTAAAGTTTA
*
3200153 GATTAAGATATTAAAGTTTA
1 GATTAAAAT-TTAAAGTTTA
3200173 TAATTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.46, C:0.00, G:0.13, T:0.41
Consensus pattern (19 bp):
GATTAAAATTTAAAGTTTA
Found at i:3208743 original size:2 final size:2
Alignment explanation
Indices: 3208736--3208788 Score: 79
Period size: 2 Copynumber: 26.5 Consensus size: 2
3208726 AGCTAACTCA
* * *
3208736 TC TC TC TC TC TC TC TC TC TC TC TC TT TC TT TC TC TC TC TT TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3208778 TC TC TC TC TC T
1 TC TC TC TC TC T
3208789 TTCAAATATA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (2 bp):
TC
Found at i:3208789 original size:14 final size:14
Alignment explanation
Indices: 3208736--3208791 Score: 94
Period size: 14 Copynumber: 4.0 Consensus size: 14
3208726 AGCTAACTCA
*
3208736 TCTCTCTCTCTCTC
1 TCTCTCTCTCTTTC
3208750 TCTCTCTCTCTTTC
1 TCTCTCTCTCTTTC
*
3208764 TTTCTCTCTCTTTC
1 TCTCTCTCTCTTTC
3208778 TCTCTCTCTCTTTC
1 TCTCTCTCTCTTTC
3208792 AAATATATCA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 39 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (14 bp):
TCTCTCTCTCTTTC
Found at i:3209421 original size:2 final size:2
Alignment explanation
Indices: 3209377--3209404 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3209367 GTTTGTAACC
3209377 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3209405 CATTTACACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3211027 original size:5 final size:5
Alignment explanation
Indices: 3211013--3211061 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
3211003 GTCCGTCCGT
* * * *
3211013 CTCGT CTCGG CTCGG CACGG CACGG CACGG CTCGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
3211062 TGGTCGTGGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.06, C:0.41, G:0.37, T:0.16
Consensus pattern (5 bp):
CTCGG
Found at i:3211070 original size:6 final size:6
Alignment explanation
Indices: 3211059--3211125 Score: 107
Period size: 6 Copynumber: 11.2 Consensus size: 6
3211049 TCGGCTCGGC
* * *
3211059 TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGAGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
3211107 TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG T
3211126 AATACGTGTC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 59 1.00
ACGTcount: A:0.04, C:0.16, G:0.49, T:0.30
Consensus pattern (6 bp):
TCGTGG
Found at i:3211425 original size:22 final size:22
Alignment explanation
Indices: 3211400--3211454 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
3211390 TCAGGAGTTA
* *
3211400 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
3211422 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
3211444 CGGGAGTTATA
1 CAGGAGTTATA
3211455 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:3216994 original size:5 final size:5
Alignment explanation
Indices: 3216980--3217028 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
3216970 GTCCGTCCGT
* * * *
3216980 CTCGT CTCGG CTCGG CACGG CACGG CACGG CTCGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
3217029 TGGTCGTGGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.06, C:0.41, G:0.37, T:0.16
Consensus pattern (5 bp):
CTCGG
Found at i:3217037 original size:6 final size:6
Alignment explanation
Indices: 3217026--3217086 Score: 95
Period size: 6 Copynumber: 10.2 Consensus size: 6
3217016 TCGGCTCGGC
* * *
3217026 TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGAGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
3217074 TCGTGG TCGTGG T
1 TCGTGG TCGTGG T
3217087 AATACGTGTC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.05, C:0.16, G:0.49, T:0.30
Consensus pattern (6 bp):
TCGTGG
Found at i:3219547 original size:22 final size:23
Alignment explanation
Indices: 3219522--3219572 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
3219512 AACCGTGACT
3219522 TTTTAATT-GCTAATTACACTTA
1 TTTTAATTAGCTAATTACACTTA
*
3219544 TTTT-ATTAAAGCTAATTACACTTT
1 TTTTAATT--AGCTAATTACACTTA
3219568 TTTTA
1 TTTTA
3219573 TTAATTAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 3 0.12
22 4 0.17
24 17 0.71
ACGTcount: A:0.31, C:0.12, G:0.04, T:0.53
Consensus pattern (23 bp):
TTTTAATTAGCTAATTACACTTA
Found at i:3219558 original size:24 final size:24
Alignment explanation
Indices: 3219530--3219576 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
3219520 CTTTTTAATT
3219530 GCTAATTACACTTATTTTATTAAA
1 GCTAATTACACTTATTTTATTAAA
*
3219554 GCTAATTACACTTTTTTTATTAA
1 GCTAATTACACTTATTTTATTAA
3219577 TTAATGCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.13, G:0.04, T:0.49
Consensus pattern (24 bp):
GCTAATTACACTTATTTTATTAAA
Found at i:3220394 original size:48 final size:48
Alignment explanation
Indices: 3220342--3221078 Score: 268
Period size: 48 Copynumber: 15.4 Consensus size: 48
3220332 CTATGAATCT
* *
3220342 TCTCCACCTCCACCATCACCTTCACCACCTCCTCCATACGTCTACAAG
1 TCTCCACCACCACCATCACCTTCACCACCTCCTCCATATGTCTACAAG
* *
3220390 TCTCCACCACCACCACCACCACCTCCATCACCATCACCCCCTCCTCCATGTGTCTACAAG
1 TCT---CCACCACCACCATCACCT---TCA-C--CA---CCTCCTCCATATGTCTACAAG
* ** ** * * *
3220450 TCTTCACCACCTTCATCACCAGCACCTCCTTCTCCTTATGTCTACAAG
1 TCTCCACCACCACCATCACCTTCACCACCTCCTCCATATGTCTACAAG
* * * *
3220498 TCCCCTCCTCCACCATCACCTTCA-CACCCTCCTCCATATGTTTACAAG
1 TCTCCACCACCACCATCACCTTCACCA-CCTCCTCCATATGTCTACAAG
* * * * * * * * * * *
3220546 TCTCCACCACCTCCTTCACCATCCCCACCACCACCTTACGTTTATAAA
1 TCTCCACCACCACCATCACCTTCACCACCTCCTCCATATGTCTACAAG
* * *
3220594 TCGT-CACTACCACCATCACCTTCACCCCCTCCTCCATATGTTTACAAG
1 TC-TCCACCACCACCATCACCTTCACCACCTCCTCCATATGTCTACAAG
** * * *** * * * * * *
3220642 TCTCCACCACCTTCTTCACCGTCTTTACCACCAT-CTTACGTTTATAAA
1 TCTCCACCACCACCATCACCTTCACCACCTCC-TCCATATGTCTACAAG
* * * * * **
3220690 TCACCACCACCTCCATCTCCATCACCTCCTCCTCTTTATGTCTACAAG
1 TCTCCACCACCACCATCACCTTCACCACCTCCTCCATATGTCTACAAG
* * * *
3220738 TC-CCATCCTCCACCTTCACCTTCA-C-TC-CCTCCATATGTTTACAAG
1 TCTCCA-CCACCACCATCACCTTCACCACCTCCTCCATATGTCTACAAG
* * *
3220783 TCTCCACCACC-TC--CACC-T--CCACCTCCAT-CACCA--TC-ACCA-
1 TCTCCACCACCACCATCACCTTCACCACCTCC-TCCA-TATGTCTACAAG
* * * *
3220822 TCCCCACCACCACCACCATCACCTTCACCCCCTCCTCCATATATTTACAAG
1 T---CTCCACCACCACCATCACCTTCACCACCTCCTCCATATGTCTACAAG
* * * * * * * * * * *
3220873 TCTCCACCACCTCCTTCACCATCTCCGCCACCACCTTACGTTTATAA-
1 TCTCCACCACCACCATCACCTTCACCACCTCCTCCATATGTCTACAAG
* * *
3220920 -AT-CACCACCA-C--CACCTTTACC-CCTTCTTCCATATGTCTACAAG
1 TCTCCACCACCACCATCACCTTCACCACC-TCCTCCATATGTCTACAAG
* ** * * *
3220963 TCTCCACCACCTCCATCACCACCA-CATCTTCCTCCTTATGTCTACAAA
1 TCTCCACCACCACCATCACCTTCACCA-CCTCCTCCATATGTCTACAAG
* * ** * *
3221011 TCCCCTCCTTCACCATCACGTTCACC-CTCTCCTCCATATGTTTACAAG
1 TCTCCACCACCACCATCACCTTCACCAC-CTCCTCCATATGTCTACAAG
* *
3221059 TCTCCACCACCTCCTTCACC
1 TCTCCACCACCACCATCACC
3221079 ATCCCCACAA
Statistics
Matches: 486, Mismatches: 153, Indels: 100
0.66 0.21 0.14
Matches are distributed among these distances:
39 1 0.00
40 4 0.01
41 5 0.01
42 35 0.07
43 3 0.01
44 3 0.01
45 39 0.08
46 7 0.01
47 11 0.02
48 306 0.63
49 7 0.01
50 3 0.01
51 18 0.04
53 1 0.00
54 5 0.01
55 1 0.00
57 15 0.03
60 22 0.05
ACGTcount: A:0.22, C:0.47, G:0.04, T:0.27
Consensus pattern (48 bp):
TCTCCACCACCACCATCACCTTCACCACCTCCTCCATATGTCTACAAG
Found at i:3220421 original size:21 final size:21
Alignment explanation
Indices: 3220391--3220438 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
3220381 GTCTACAAGT
*
3220391 CTCCACCACCACCACCACCAC
1 CTCCATCACCACCACCACCAC
* * *
3220412 CTCCATCACCATCACCCCCTC
1 CTCCATCACCACCACCACCAC
3220433 CTCCAT
1 CTCCAT
3220439 GTGTCTACAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.62, G:0.00, T:0.15
Consensus pattern (21 bp):
CTCCATCACCACCACCACCAC
Found at i:3220470 original size:60 final size:60
Alignment explanation
Indices: 3220345--3220460 Score: 169
Period size: 60 Copynumber: 1.9 Consensus size: 60
3220335 TGAATCTTCT
* * *
3220345 CCACCTCCACCATCACCTTCACCACCTCCTCCATACGTCTACAAGTCTCCACCACCACCA
1 CCACCACCTCCATCACCATCACCACCTCCTCCATACGTCTACAAGTCTCCACCACCACCA
* ** *
3220405 CCACCACCTCCATCACCATCACCCCCTCCTCCATGTGTCTACAAGTCTTCACCACC
1 CCACCACCTCCATCACCATCACCACCTCCTCCATACGTCTACAAGTCTCCACCACC
3220461 TTCATCACCA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.23, C:0.53, G:0.04, T:0.20
Consensus pattern (60 bp):
CCACCACCTCCATCACCATCACCACCTCCTCCATACGTCTACAAGTCTCCACCACCACCA
Found at i:3220551 original size:42 final size:42
Alignment explanation
Indices: 3220505--3220650 Score: 121
Period size: 42 Copynumber: 3.2 Consensus size: 42
3220495 AAGTCCCCTC
3220505 CTCCACCATCACCTTCACACCCTCCTCCATATGTTTACAAGT
1 CTCCACCATCACCTTCACACCCTCCTCCATATGTTTACAAGT
* * * * * *
3220547 CTCCACCACCTCCTTCACCATCCCCACCACCACCTTACGTTTATAAATCGT
1 CTCCACCATCACCTTCA-CA--CCCTCCTCCA---TATGTTTA-CAA--GT
*
3220598 CACTACCACCATCACCTTCACCCCCTCCTCCATATGTTTACAAGT
1 --CT-CCACCATCACCTTCACACCCTCCTCCATATGTTTACAAGT
3220643 CTCCACCA
1 CTCCACCA
3220651 CCTTCTTCAC
Statistics
Matches: 79, Mismatches: 13, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
42 21 0.27
43 4 0.05
45 10 0.13
47 2 0.03
48 14 0.18
49 2 0.03
51 10 0.13
53 3 0.04
54 13 0.16
ACGTcount: A:0.24, C:0.46, G:0.04, T:0.26
Consensus pattern (42 bp):
CTCCACCATCACCTTCACACCCTCCTCCATATGTTTACAAGT
Found at i:3220672 original size:96 final size:96
Alignment explanation
Indices: 3220403--3220757 Score: 343
Period size: 96 Copynumber: 3.7 Consensus size: 96
3220393 CCACCACCAC
* * * * * * *
3220403 CACCACCACCTCCATCACCATCACCCCCTCCTCCATGTGTCTACAAGTCTTCACCACCTTCATCA
1 CACCACCACCACCATCACCTTCACCCCCTCCTCCATATGTTTACAAGTCTCCACCACCTCCTTCA
* * * ** * * * * *
3220468 CCAGCACCTCCTTCTCCTTATGTCTACAAGT
66 CCATCCCCACCACCACCTTACGTTTATAAAT
* * * *
3220499 CCCCTCCTCCACCATCACCTTCACACCCTCCTCCATATGTTTACAAGTCTCCACCACCTCCTTCA
1 CACCACCACCACCATCACCTTCACCCCCTCCTCCATATGTTTACAAGTCTCCACCACCTCCTTCA
3220564 CCATCCCCACCACCACCTTACGTTTATAAAT
66 CCATCCCCACCACCACCTTACGTTTATAAAT
** * *
3220595 CGTCACTACCACCATCACCTTCACCCCCTCCTCCATATGTTTACAAGTCTCCACCACCTTCTTCA
1 CACCACCACCACCATCACCTTCACCCCCTCCTCCATATGTTTACAAGTCTCCACCACCTCCTTCA
* *** *
3220660 CCGTCTTTACCACCATCTTACGTTTATAAAT
66 CCATCCCCACCACCACCTTACGTTTATAAAT
* * * * ** * * *
3220691 CACCACCACCTCCATCTCCATCACCTCCTCCTCTTTATGTCTACAAGTC-CCATCCTCCACCTTC
1 CACCACCACCACCATCACCTTCACCCCCTCCTCCATATGTTTACAAGTCTCCA-CCACCTCCTTC
3220755 ACC
65 ACC
3220758 TTCACTCCCT
Statistics
Matches: 212, Mismatches: 46, Indels: 2
0.82 0.18 0.01
Matches are distributed among these distances:
95 3 0.01
96 209 0.99
ACGTcount: A:0.22, C:0.46, G:0.05, T:0.28
Consensus pattern (96 bp):
CACCACCACCACCATCACCTTCACCCCCTCCTCCATATGTTTACAAGTCTCCACCACCTCCTTCA
CCATCCCCACCACCACCTTACGTTTATAAAT
Found at i:3220757 original size:42 final size:45
Alignment explanation
Indices: 3220711--3220808 Score: 103
Period size: 45 Copynumber: 2.2 Consensus size: 45
3220701 TCCATCTCCA
** *
3220711 TCACCTCCT-CCTCTTTATGTCTACAAGTC-CCA-TCCTCCACCT
1 TCACCTCCTCCCTCCATATGTCTACAAGTCTCCACACCTCCACCT
*
3220753 TCACCTTCACTCCCTCCATATGTTTACAAGTCTCCACCACCTCCACCT
1 TCACC-TC-CTCCCTCCATATGTCTACAAGTCTCCA-CACCTCCACCT
*
3220801 CCACCTCC
1 TCACCTCC
3220809 ATCACCATCA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
42 5 0.11
43 2 0.04
44 2 0.04
45 17 0.38
46 4 0.09
47 2 0.04
48 13 0.29
ACGTcount: A:0.18, C:0.48, G:0.04, T:0.30
Consensus pattern (45 bp):
TCACCTCCTCCCTCCATATGTCTACAAGTCTCCACACCTCCACCT
Found at i:3220816 original size:6 final size:6
Alignment explanation
Indices: 3220807--3220850 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
3220797 ACCTCCACCT
* * * *
3220807 CCATCA CCATCA CCATCC CCACCA CCACCA CCATCA CCTTCA CC
1 CCATCA CCATCA CCATCA CCATCA CCATCA CCATCA CCATCA CC
3220851 CCCTCCTCCA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.27, C:0.59, G:0.00, T:0.14
Consensus pattern (6 bp):
CCATCA
Found at i:3220829 original size:30 final size:30
Alignment explanation
Indices: 3220787--3220856 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
3220777 TACAAGTCTC
* *
3220787 CACCACCTCCACCTCCACCTCCATCACCAT
1 CACCACCTCCACCACCACCACCATCACCAT
*
3220817 CACCATCC-CCACCACCACCACCATCACCTT
1 CACCA-CCTCCACCACCACCACCATCACCAT
*
3220847 CACCCCCTCC
1 CACCACCTCC
3220857 TCCATATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
29 2 0.06
30 30 0.88
31 2 0.06
ACGTcount: A:0.23, C:0.63, G:0.00, T:0.14
Consensus pattern (30 bp):
CACCACCTCCACCACCACCACCATCACCAT
Found at i:3220926 original size:90 final size:91
Alignment explanation
Indices: 3220831--3221081 Score: 270
Period size: 90 Copynumber: 2.7 Consensus size: 91
3220821 ATCCCCACCA
*
3220831 CCACCACCATCACCTTCACCCCCTCCTCCATATATTTACAAGTCTCCACCACCTCCTTCACCATC
1 CCACCACCATCACCTTCACCCCCTCCTCCATATGTTTACAAGTCTCCACCACCTCCTTCACCATC
* * * *
3220896 TCCGCCACCACCTTACGTTTATAAAT
66 ACAGCCACCACCTTACGTCTACAAAT
* * * * * * *
3220922 -CACCACCACCACCTTTACCCCTTCTTCCATATGTCTACAAGTCTCCACCACCTCCATCACCACC
1 CCACCACCATCACCTTCACCCCCTCCTCCATATGTTTACAAGTCTCCACCACCTCCTTCACCATC
* ** * *
3220986 ACATCTTCCTCCTTATGTCTACAAAT
66 ACAGCCACCACCTTACGTCTACAAAT
* * *
3221012 CCCCTCCTTCACCATCACGTTCACCCTCTCCTCCATATGTTTACAAGTCTCCACCACCTCCTTCA
1 --CC-AC--CACCATCACCTTCACCCCCTCCTCCATATGTTTACAAGTCTCCACCACCTCCTTCA
3221077 CCATC
61 CCATC
3221082 CCCACAACCA
Statistics
Matches: 127, Mismatches: 27, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
90 73 0.57
93 1 0.01
94 1 0.01
96 52 0.41
ACGTcount: A:0.23, C:0.46, G:0.04, T:0.27
Consensus pattern (91 bp):
CCACCACCATCACCTTCACCCCCTCCTCCATATGTTTACAAGTCTCCACCACCTCCTTCACCATC
ACAGCCACCACCTTACGTCTACAAAT
Found at i:3221085 original size:258 final size:259
Alignment explanation
Indices: 3220816--3221411 Score: 761
Period size: 255 Copynumber: 2.3 Consensus size: 259
3220806 TCCATCACCA
3220816 TCACCATCCCCACCACCACCACCATCACCTTCACCCCCTCCTCCATATATTTACAAGTCTCCACC
1 TCACCATCCCCA-CACCACCACCATCACCTTCACCCCCTCCTCCATATATTTACAAGTCTCCACC
* * * *
3220881 ACCTCCTTCACCAT-CTCCGCCACCACCTTACGTTTATAAATCACCACCACCACCTTTACCCCTT
65 ACCTCATTCACCATCCT-CACCACCACCTTACGTTTACAAATCACCACCACCACCTTTACCCCCT
* * * * *
3220945 CTTCCATATGTCTACAAGTCTCCA-C-CACCTCCATCACCACCACATCTTCCTCCTTATGTCTAC
129 CCTACATATATCTACAAGTCTCCACCACACCTCCATCACAACCACATCATCCTCCTTATGTCTAC
* *
3221008 AAATCCCCTCCTTCACCATCACGTTCACCCTCTCCTCCATATGTTTACAAGTCTCCACCACCTCC
194 AAATCCCCTCCTTCACCATCACGTTCACCCCCTCCTCCATATATTTACAAGTCTCCACCACCTCC
3221073 T
259 T
* *
3221074 TCACCATCCCCACA--ACCACCATCACATTCATCCCCTCCTCCATATATTTACAAGTCTCCACCA
1 TCACCATCCCCACACCACCACCATCACCTTCACCCCCTCCTCCATATATTTACAAGTCTCCACCA
* *
3221137 CCTCATTCACCCTCCTCACCACCATCTTACGTTTACAAATCACCACCACCACCTTTACCCCCTCC
66 CCTCATTCACCATCCTCACCACCACCTTACGTTTACAAATCACCACCACCACCTTTACCCCCTCC
* ** * * *
3221202 TACATATATCTACATGTCTCCACCATCACCTCCATCTTAATCACCTCATCCTCTTTATGTCTACA
131 TACATATATCTACAAGTCTCCACCA-CACCTCCATCACAACCACATCATCCTCCTTATGTCTACA
* * * * *
3221267 AGTCTCCTCCTTCGCCATCACTTTCACCCCCTCCTCCATATATTTACAAGTCTCCACTACCTCCT
195 AATCCCCTCCTTCACCATCACGTTCACCCCCTCCTCCATATATTTACAAGTCTCCACCACCTCCT
** * * *
3221332 TACATTTATAAATCACCACCAACACCAACACCATCACCTTCACCCCCTCCTCCATATGTCTACAA
1 T-C----A-CCAT--CC-CC-ACACCACCACCATCACCTTCACCCCCTCCTCCATATATTTACAA
3221397 GTCTCCACCACCTCA
56 GTCTCCACCACCTCA
3221412 ATCTTTATCA
Statistics
Matches: 289, Mismatches: 33, Indels: 20
0.85 0.10 0.06
Matches are distributed among these distances:
255 121 0.42
256 3 0.01
257 2 0.01
258 103 0.36
259 1 0.00
263 1 0.00
264 2 0.01
266 2 0.01
267 2 0.01
268 3 0.01
270 49 0.17
ACGTcount: A:0.24, C:0.45, G:0.03, T:0.27
Consensus pattern (259 bp):
TCACCATCCCCACACCACCACCATCACCTTCACCCCCTCCTCCATATATTTACAAGTCTCCACCA
CCTCATTCACCATCCTCACCACCACCTTACGTTTACAAATCACCACCACCACCTTTACCCCCTCC
TACATATATCTACAAGTCTCCACCACACCTCCATCACAACCACATCATCCTCCTTATGTCTACAA
ATCCCCTCCTTCACCATCACGTTCACCCCCTCCTCCATATATTTACAAGTCTCCACCACCTCCT
Found at i:3221135 original size:42 final size:42
Alignment explanation
Indices: 3221089--3221226 Score: 114
Period size: 42 Copynumber: 3.1 Consensus size: 42
3221079 ATCCCCACAA
* *
3221089 CCACCATCACATTCATCCCCTCCTCCATATATTTACAAGTCT
1 CCACCACCACATTCACCCCCTCCTCCATATATTTACAAGTCT
* * * * *
3221131 CCACCACCTCATTCACCCTCCTCACCACCATCTTACGTTTACAAATCA
1 CCACCACCACATTCACCC-CCT--CCTCCAT-ATA--TTTACAAGTCT
* * * * *
3221179 CCACCACCACCTTTACCCCCTCCTACATATATCTACATGTCT
1 CCACCACCACATTCACCCCCTCCTCCATATATTTACAAGTCT
3221221 CCACCA
1 CCACCA
3221227 TCACCTCCAT
Statistics
Matches: 73, Mismatches: 17, Indels: 12
0.72 0.17 0.12
Matches are distributed among these distances:
42 28 0.38
43 3 0.04
44 2 0.03
45 11 0.15
46 2 0.03
47 3 0.04
48 24 0.33
ACGTcount: A:0.26, C:0.45, G:0.02, T:0.27
Consensus pattern (42 bp):
CCACCACCACATTCACCCCCTCCTCCATATATTTACAAGTCT
Found at i:3221766 original size:48 final size:49
Alignment explanation
Indices: 3221722--3221832 Score: 154
Period size: 48 Copynumber: 2.3 Consensus size: 49
3221712 TTCTTATATT
* *
3221722 TATAAGTCTTCACCACCTCCAGTCCACTCTCGACCTCGT-CCTTATGTC
1 TATAAGTCTCCACCACCTCCAGTCCACTCACGACCTCGTCCCTTATGTC
* ** *
3221770 TATAAGTCTCCACCACCTCCATTTTACTCACGACCTCGTCCCTT-TGTG
1 TATAAGTCTCCACCACCTCCAGTCCACTCACGACCTCGTCCCTTATGTC
3221818 TATAAGTCTCCACCA
1 TATAAGTCTCCACCA
3221833 ACCCATTCAC
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
48 52 0.93
49 4 0.07
ACGTcount: A:0.21, C:0.38, G:0.10, T:0.32
Consensus pattern (49 bp):
TATAAGTCTCCACCACCTCCAGTCCACTCACGACCTCGTCCCTTATGTC
Found at i:3225519 original size:21 final size:21
Alignment explanation
Indices: 3225493--3225535 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3225483 TTTCTGGGTT
* *
3225493 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
3225514 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
3225535 A
1 A
3225536 CGAAATGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:3225654 original size:69 final size:68
Alignment explanation
Indices: 3225515--3225668 Score: 195
Period size: 70 Copynumber: 2.2 Consensus size: 68
3225505 ACCCATTCAA
* * *
3225515 GGGGAACCGATACCCCTTCAACGAAATGAATTTCCAGAATGCAAGAGGGGAATAGATACCCCAAG
1 GGGGAACCGATACCCCCTCAACGAAATGAAATTCCAGAATGCAAGAGGGGAACAGATACCCCAA-
3225580 GGGG
65 GGGG
* * * *
3225584 GGGGAACCGATACCCCCTCATCGTATAA-GAAATTCCAGAATGCTATAGGGGAACCGATACCCC-
1 GGGGAACCGATACCCCCTCAACG-A-AATGAAATTCCAGAATGCAAGAGGGGAACAGATACCCCA
3225647 AGGGG
64 AGGGG
*
3225652 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
3225669 ATGAGAAAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
68 20 0.27
69 22 0.29
70 31 0.41
71 2 0.03
ACGTcount: A:0.31, C:0.26, G:0.28, T:0.15
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGAAATGAAATTCCAGAATGCAAGAGGGGAACAGATACCCCAAG
GGG
Done.